We are developing a new potential for protein fold recognition from sequence, using high-order (beyond pairwise) interactions of residues in th protein chain. Such interactions contribute significant information for fold-recognition, which is required to improve the performance of current "protein-threading" algorithms. We have also developed a new technique based on hidden Markov models (HMMs) which can recognize the topology or general shape of a protein from its amino acid sequence. The method makes use solely of secondary structure potential information encoded in each sequence, and attempts to match a secondary structure prediction to a library of HMMs which represent the known topology families. A catalogue of all "linkers" in protein structures was prepared. Linkers ar loops that connect regular secondary structural elements (strands and helices), and may play an important role in the protein structure and function. Using a sequential clustering approach, we were able to characterize many classes of linkers, beyond the well-known beta hairpins. Amino-acid preferences for certain sites on each linker class were computed and may be useful for eventual prediction of linker conformation. We have used molecular dynamic simulation and energy minimization to investigate th conformation of beta-turns in the context of the aqueous environment of a complete protein structure. The goal was to determine the source of the preference for assuming each turn type (I, I', II, II') for each of several structures. Energies were calculated for the native turn and for several non-native types. Another study used a novel descriptive method for protein chain conformation to describe naturally occurring distortions found in otherwise ideal alpha-helices. The study ascribed such distortions to the presence of certain residues within the helix, or to "packing forces" exerted by other parts of the molecule. Much of our earlier work on protein secondary structure prediction methods is now available as a WWW-based service. Investigators on the Internet may utilize our Quadratic-Logistic prediction program and obtain automatic homolog searching of the NCBI databases, automatic alignment of homologs, and conversion between various data formats. A major conference, ~Protein Folding and Design," sponsored b DCRT and by the Fogarty International Center, was organized by Dr. Garnier, and hosted by the ABS. This conference was highly successful, drawing the largest attendance of any such conference at NIH. We have continued the development of the MUSEQAL Iterative Multiple Sequence Alignment Program, and demonstrated its utility in finding improved alignments on two well- studied families (globins and seven-transmembrane helix receptor proteins). The ABS continues to provide statistical consultation and support for investigators at NIH. In particular, users of programs LIGAND, ALLFIT and PULSEFIT were assisted.